Why, and on which line, do you expect to see $5,138 (a number not obviously related to any of the numbers in your details)?

Nondeductible expense gets backed out of basis on Line 8a, unless you've elected to deduct losses before non-deductible expense, in which case it gets backed out of basis on Line 13. If you made that election, you should enter a 1 in the line of the Basis Limitation (7203) input, where it says "1=deduct losses before nondeductible expenses and depletion."